Here is the sequence logo predicted by the SAM server:

H = helix
E = sheet
C = loop (or coil)

The taller the letter at each position, the higher the probability of that specific secondary structure for that amino acid.

For example, the Valine at residue 107 is highly predicted to be part of a helix. However, the Valine at residue 137 is predicted to be in a sheet!

The above predictions are already on the starting model (based on the horizontal lines in the above figure).
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Cutaway view hint:
If you hover your mouse over a segment and type shift-Q, the game will hide parts of the protein and cloud that are not in the same plane as that segment - it cuts down on how much cloud you see at one time and makes it easier to focus. Q returns to normal view.
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New Electron Density Features:

- Notes can be added to the electron density if present. To add one, press TAB with the mouse over the density while the density panel is open. Use the recycle button in the note panel to erase one. (Note: saving and sharing these notes is a feature that should be in a future release)

- There is a button in the Electron Density Panel to focus rotation on the density. You can use the HOME or Q keys to refocus on the protein.
- The density score of a residue may now be viewed in the tab menu
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Because this is the first time we are combining Electron Density and the Alignment Tool, you'll notice that when you thread your sequence onto a template, it is nowhere near the density. If you want everything in the same place, after threading you can use the "Align Protein to Density" button in the Electron Density Panel and then press Q.

The above video from our YouTube channel has Seth Cooper explaining how to add Notes to the electron density.

Here is a link to our channel if you want to see other videos:
http://www.youtube.com/user/UWfoldit

why the initial structure is not the sam prediction?

Wow... somehow the pdb file got corrupted in the posting process, that has never happened before!

I will have to repost this one as 741b (allowing you to load in your manual saves from this puzzle).

I'm sorry about this (I had quickly checked to make sure there WERE ss predictions on the extended chain, and assumed they were the ones I had assigned from SAM!), thanks again for reporting it!